The Alpha Project
by Alexander the seventy-fifth
Summary: Rewrite. In Rapture, there was something Ryan never talked about, never borught up in any other place then his labs. It was a secret, a dark secret that could have spelled the end of all he'd made. And as it would seem, he didn't hide it well enough.


**A/N So. I'm back. Crazy huh? I've been a little busy lately, with finishing school and all, but now that it's summer, and I have some more time to work with, I can start writing again. This is a rewrite/revision of the earlier version. I didn't like how it turned out so I decided that I'd just go through and do it over, see if it's better this time. But, I may not update for a while yet, i.e. next week. Because I won't be around my computer all of that week, but, I will be using a notebook to draft out and finalize the next chapters so I'll at least have an update by the following Monday, maybe. I hope that I can get in a third chapter before I have to leave again after that. I'm sorry, it's just the way it worked out, but I think before the end of August I'll have the fifth or sixth chapter done. Anyways, enjoy the story, I worked hard, and please leave a review. I tired to make this as good as I could but your comments are needed for me to know if I'm doing it right. Thanks.**

In the depths of the sea, underneath the massive crushing force of the ocean's waters, there is said to be a vast utopia. A city built underwater, created right under the unsuspecting gaze of all of the world powers. It was a place that held those who wished to escape the hands of the government, who wished to escape the pressure of a controlled society based on a set of morals that were created centuries ago. These people defied the ethics of the society above, did as they always wanted to above in the city below, creating a new society. Rapture. The city under the ocean, free of moral and ethic, free of bondage and enslavement, and free of control.

For a while it's creators seemed to be in control, they had a look of superiority, the look of leaders. But no one knew what was happening behind the masks, no one knew of the secrets they hid from the outside. Not a single person out side of their own labs knew of what the city's creator was making. This was the Alpha Project. The project span from many points, Plasmids, Protectors, Gatherers. But it ended up as one subject, one _person_ who became the center of their industry. This person _became_ the Alpha Project, became the collection of all their experiments, and was transformed into Andrew Ryan's perfect monster. Andrew Ryan desired a city free of law and god, free of oppression, but instead, he created Rapture.

Alpha Project: Chapter One.

The darkness never bothered the Little Sisters. Never, not even once were they afraid of the dark, and rightfully so. With the Big Daddies they were all but untouchable, perfectly safe under the watchful eye of their faithful guardians. But at the moment, this one Little Sister was by herself, alone in the dark corridor that led further into the abyss. The girl sang happily as she skipped down the dark, twisting path downwards, her hands clutching onto the gun-like syringe like it was her favorite toy. Her glowing eyes danced along merrily, not seeing the blood stained walls or the broken bodies that lay in her path.

Her steps kept leading her downward, her voice carrying through the halls. She was excited, more excited than when Mr. Bubbles came with her on an adventure to look for angles. Today she was going to visit 'The Room' again, as she'd done for many days previous. She was always excited to come down here and visit 'The Room'. It wasn't the room itself however, but what it contained. Because inside the room there was a table, a long table with many bright ribbons and flowing, soft cloth. And on this table rested an Angel, an Angel that wasn't like all the others.

This Angel was different; he didn't smell like an Angel, he smelt kind of like Mr. Bubbles. His smell made her feel safe, gave her a kind of warmth inside, and she didn't know why. But from the Adam she'd gathered she found that the feeling was so much like when an Angel was with their 'Daddy'. And so, she'd named the strange Angel she'd found, Daddy. Sometimes she'd come down to talk with him, to tell him stories about the Angels and Mr. Bubbles. She'd talk about the other girls and what they talked about; she'd sometimes draw on the floor making doodles of Mr. Bubbles in his shining armor, or of Big Sister in her armor. And sometimes, she'd lie down next to him, and sleep. She could sleep for hours next to her Daddy, the one Angel who made her feel even more special than when she was with Mr. Bubbles. She felt safe with him.

So as she skipped down the familiar hallways, singing a bright tune, she started to think harder. She'd never gotten him to wake up before, the other Angels danced all the time with Mr. Bubbles, they got up and sang with him, dancing in circles and circles. But some of the Angels were bad; they tried to get her away from Mr. Bubbles. And when they did Mr. Bubbles got angry and knocked them around giving the stars and birdies around their heads. But why wouldn't her Daddy get up and play with her? She tried to get him of the table he was on, but he wouldn't budge, their were ribbons tied around him with tight bows that she couldn't break. Other things were on him too, colorful lights and buzzers, and a halo that was put down onto his head.

As she rounded the corner she saw the opening to the Angel's room, a gap in the wall that was blown open years ago and never touched afterwards. She walked over to it, carefully stepping over the low part of the wall that was left there. Her feet smacked the ground loudly as she entered the quiet room, the dead silence not bothering her in the slightest. She stepped forward without hesitation, confident that she knew exactly what was waiting for her in the room. As she walked forward the darkness revealed the shining glow of her Daddy, his limbs tied down to the table with ribbons of red fabric. She approached him without a falter in her step, seeing a fine, almost expensive, looking suit on him instead of the ragged clothing that was reality.

She looked up to his face and smiled at the Angel, he was just as calm as ever, a perfectly set face with his eyes closed restfully. She looked up further on his head, to the halo that encircled it. As she starred, an idea formed. A glorious, completely ingenious idea. She grabbed a gleaming gold pole from the ground, not wanting to dent her harvesting needle. She lifted the pole up, aiming carefully as to not damage her Daddy, and slammed the pole onto his halo. The halo cracked, beginning to sparkle and dance with different shades of many colors shining in every direction. The bright lights began to increase as the halo cracked some more, making a hissing sound as it did. And the halo cracked into two pieces, one falling to each side of him head.

She watched him patiently, getting more and more excited as the seconds passed. When the ribbons keeping him down snapped off she squealed, he was going to wake up! She knew it, her thoughts raced harder and faster as he began to stir, the anticipation causing her to fidget where she sat, unable to sit still as she had always done. And then, he opened his eyes.

00100

Darkness. It was all that surrounded him in the place he was in, a place in-between the world of dreams and the awakened world. He seemed to float there, his body numb and unfeeling, thoughts blank and clouded, appearing as burst of wind around him in his black place. He tried to remember, to remember anything, anything at all. How did he get here? Why couldn't he feel anything? Who was he?

His lack of memories disturbed him; no names came to his mind as he searched his mind for answers. No memories flashed upon his inner screen, only a blank canvas of nothing falling in around him. He tried to move, anything at all, trying desperately to at least do something. But his body wouldn't respond to his commands. As much as he tried he couldn't do anything. It frustrated him, being unable to move, unable to remember, completely disabled from himself. All he could do was stare blankly into whatever darkness surrounded him, if his eyes were even open, and wonder how long he'd been there.

He let his swirling thoughts rest as he slowly realized the futility of his situation. He was a guest to what ever dark thing kept him here, to whatever creature or happening that bound him to this world of nothing. And as he lay there, resting himself within his mind, he felt something. A small pinprick crawling down his spine, a tiny little prick that roused him. The pinprick was followed by another, and then yet another, each time it was more frequent, more alarming. The area they cover spread rapidly, coursing down his spine and branching out onto the rest of his body. And soon he felt them every where.

The pricks faded into a tingling sensation that covered him, all of him. His mind went numb, unable to think as something pulled on his consciousness, a foreign force that pulled so much harder than anything he'd ever felt. The force pulled his consciousness outwards in all directions, expanding it until it finally collapsed into itself and snapped back into place around him. He felt air upon him; cool breezing that ran down his skin like frost on glace. He shivered from the new sensation, remembering it yet not.

He stopped suddenly, he had felt something. His body was able to feel again! He was free from that dark cage he had been imprisoned in. He roused himself, trying anxiously to get himself to move. His arms twitched, muscles cramped and tense from lack of use. He slowly moved them, beginning to get back his motor skills. He tested his fist, feeling it curl and uncurl. It was then he noticed that he had yet to open his eyes, yet to see where he was. And so, slowly, apprehensively, he opened them. As his eyelids slid open, he saw blurred objects, completely out of focus, not even a definite shape. But as he blinked his eyes, slowly and deliberately, he began to focus on what surrounded him.

He saw a room, a dark room with only a single lamp beside where he had been unconscious. He found that he was lying on a table of sorts, metal restraints unlocked around his limbs, hanging uselessly from the table. He was wearing some kind of cloth, a grey material that was smooth and thick. It was ripped in places and had seams cut into it to mark where it became separate garments on his upper and lower body. He looked onward, casting his gaze lazily throughout the room, the haze of his deep sleep still being driven out. He noted the blankness of the room, how there seemed to be nothing other than the table that had restrained him and himself there. And then he met the glowing gaze of the girl standing next to the table on which he had being sitting.

He locked his eyes with hers, the glowing eyes staring back at him with an emotion, an emotion he couldn't recognize. It was a mixture, showing adoration and glee all at the same time, and overload of joy that made it unintelligible. He looked the girl over; she appeared to be seven years old. He stopped for a second, unsure of just how he knew that, how could he? He tried to find doubt in his assumption but something, an old instinct, told him that he was irrevocably right. She was wearing a tattered dress, it's color long since faded and the fabric torn in places.

Her feet were bare, completely exposed to the harsh metal ground on which she currently stood. In her hands he saw a large needle, a kind of gun mechanism rigged on the large needle for extracting something. A large bottle was at the opposite end of the large needle gun, it even had a rubber cap like an infant's bottle. There were traces of a strange red liquid inside of it, it glowed and pulsed with a dim light. He returned to her gaze just in time to see her grin madly and throw herself onto him.

He felt her small arms wrap around his waist as far as they could, squeezing him as hard as her little arms could. Her head nuzzled into his stomach as she hugged him, a delighted hum loudly pronounced as she squeezed him harder. He could hear something, a tone perhaps, that distorted the voice of the little girl. It was not something he could describe, it was out of place, a thing that he knew shouldn't be there. His own arms wrapped around her form, as some part of him awakened from her embrace. It sent a surge of feeling through him, echoing down deep into him. It was a command, to protect this girl. It was etched into his entire body, a simple need to be there for her as a loving guardian, to watch out for her like she was his own daughter.

"Daddy!" She squealed, "Daddy your awake!"

He furrowed his brow at this, was he her father? Could he actually be this girl's 'Daddy'? He looked down at her, meeting her two glowing eyes once more. He tried to speak, to ask her if he was actually her father, but he couldn't get his voice to work. His body hadn't been used for so long that his muscles weren't able to form words yet.

The girl got off of him, giggling, "Come on Daddy! Let's go play with the Angels!" She picked up his hand and tugged on it, wanting him to come with her. Slowly, with much effort, he rose to his feet, using his legs for the first time since he didn't know when. His muscles screamed, wanting to continue their rest, but he relented. He pushed himself off the table and started to walk, his steps were wobbly, his legs unsteady at first. But after only a few strides he was steady, confident in his ability to move with coordination. He looked to the girl as she reached over and grasped his hand smiling up at him. "C'mon Daddy."

There was something, he didn't know what, but there was something behind everything this girl did. It was so different and powerful, he didn't know what to call it but, he just couldn't leave the girl. He felt this unavoidable adoration for her, as if she was his own daughter. _Is she my daughter?_ He smiled back down at her, an unconscious reaction to the feeling her distorted voice created, and nodded. He was aware of what was happening, he knew that the girl was not a normal child. Normal children didn't carry needles like hers, didn't have pale, almost deathly, skin, and he knew that they didn't have those strange glowing eyes.

He pondered, wondering about different, aimless things as the girl led him down the hallways. She sung a song, it was about Angels and someone named Mr. Bubbles dancing. _Who's Mr. Bubbles?_ As they walked he took in his surroundings. It seemed that he was in a building completely made from metal, with different textures flowing into each other from pressure. He spotted old, crusting pools of blood gathered on the walls and floor, bullet holes and burn marks accompanying them in equal measure. There were bodies as well, different forms of the deceased, all in different stages of decay with their dying screams frozen upon their faces.

He turned his gaze from the fallen, trying to focus on something different, something other than the death that he found himself surrounded by. And so he kept his eyes set forward, unconsciously running them over every object for any sign of an ambush or attack. All these precautions though, they confused him. Why would he need to know these things? What had he been before that had made him be this way? And as always, no answers came, only a clean and black slate of consciousness that blocked out all of his memories.

He turned his head to the girl once more as she let out a low yawn, her eyes drooping in the dim hallway lighting. "Daddy I'm tired." She said to him. He looked down at her and nodded, acknowledging her in the only way he knew how. She walked over to the wall on his right, yawning once more and then sitting down with her needle on the ground next to her. "C'mon Daddy," she beckoned him, holding out her arms in his direction. Slowly, almost cautiously, he made his way to her side, sitting in the open space beside her. As he sat down she scooted over to him and wrapped her arms around his right, holding onto him tightly as she went to sleep. He tried to stay awake, to keep his eyes open to watch for any coming danger, but failed as sleep over took him.

00100

His head was dazed when he awoke; his mind filled with static thoughts and mixed up senses. He was lying on the floor, his head in some kind of sticky substance, and an absence of two tight little arms on his right. His mind shot into overdrive, a burst of thoughts, each of a different scenario that could have led to the absence of those arms. The possibilities swam for a second before he locked in on a sound near him. He listened, intently, paying attention to any patterns that were formed by the sounds. He heard scuffling, _feet_, a sharp scrape of a piece of rubber against the ground, _shoes_, and then a loud smack of skin against skin. _A struggle. _

His eyes shot open, sharp eyes scanning and taking in his new surroundings in seconds. He was still in the hallway, the same decayed hall that the girl had taken him down, filled with blood and gore. Two feet away from him were two men, one held a heavy lead pipe while the other was closer to him, struggling with someone. The scuffles of bare feet had come from the girl, her feet dragging against the ground in an effort to resist the man holding her. Honestly, he hadn't the slightest idea why these men were here, why they were trying to take her, and what they'd hoped to accomplish. But for him it didn't matter, they were taking the only person he knew, not to mention the fact that this person had set off something in him that made him think of her as his own daughter.

His instinct kicked in, a pattern of movements that came to him naturally, kind of like an old habit that suddenly came back. And so within a second the muscles in his right leg tensed and shot out to the man struggling with the girl, hooking into the back of the man's knee and bringing him down to the floor. He got up, moving in quick, decisive movements, deliberately making each blow powerful and strong. He turned to the other man who was raising the pipe towards him. The man swung at him, a wild swing with all of the man's power backing it up, but somehow, it seemed slow to him. The blow came at him slow enough for him to analyze the man for half a second and then react. The blow came down but never connected, whizzing through the air only to be stopped by a twisting hand of his own.

He grabbed the pole, twisting it at it's base and using the momentum of the swing along with his own to rip it out of the other man's grip. The pole swung easily in his hand, striking out at the underside of the man's ribs and then slamming down onto his shoulder in an encore. The blows crushed bones, cracking and grinding the inner framework of the man's body like twigs under his fist. The man cried out in pain as the wounds registered, his mind relaying the damage back to his conscious. He struck again, a powerful blow to the back of the man's neck, severing the spinal column and snapping the nerve center there. The man's body fell to the ground like a sack of waste, flopping over with a wet thud into a pool of water.

He turned, his attention back upon the man trying to take the girl. His eyes fell upon the man's own as he was trying to stand, shaky steps that were taken towards him. He saw no fear in the man's eyes, only a maddened drive, a lunatic's need to go on passed where he knew he would die. The man launched himself at him, raking his hands towards his face. He turned, using the pole to smash into the man's back along with his freehand to grab the man and control his direction. He sent the man to the ground, the mid point of his spinal cord snapped into pieces. The man laughed, reaching his hand out towards him before he was brutally cut off by the lead pipe slamming against his head. He watched as the pipe imbedded itself slightly into the man's skull, the metal yielding slightly from the force of the blow.

He turned his gaze from the dead men, not needing to see their dying corpses to know that they were dead. Every blow he'd dealt in the past seconds had been designed to wound and kill his enemy, and he knew that. It was an efficiency he had developed at sometime or another, while he'd had his memories. And he didn't know why. But aside from the strange skills he had, there was one thing more important, the girl. He looked at her, checking her for any injuries she may have sustained during the struggle. And to his surprise, there were none. She didn't have a single mark on her, not a bruise or scratch or wound of any kind, she was completely unharmed.

This confused him as much as consoled him; how could she not have been bruised by the man's grip, at least? She was struggling hard enough for at least something to be strained or for her have defensive wounds at least, but she didn't. It was strange, like a lot of things he'd seen lately, and unnatural, but it didn't matter. She was alive and well, and that's all he cared about, all he could care about at this point. He couldn't think of anything other than protecting her, taking out anything that might try and hurt her.

"I'm always safe with Daddy," she said, smiling up at him brightly. She reached over quickly and grabbed his hand, her small fingers curling around his own. "C'mon Daddy, we're gonna miss the angels dancing!" She pulled on his hand, leading him forward down the hallway, the same direction as before. He let himself be led, finding nothing in him that could contradict the impulse to do as she said and appease her. He smiled, a true genuine smile, one that held the loving adoration of a father and peace of a restful man's mind. While he was with this girl he would be okay, while he was with her his life was complete, almost as if she was what he had been looking for. Only question was; when had he been searching for her?

He shook his head lightly, wiping the mixed up and confusing thoughts from his mind. That didn't matter now, all that was left was him and this girl. And for now at least, it would have to do. Because right now, he didn't have too many options, nor did he care to.

**A/N Well, what do you think? Leave a review on your way out please and thanks for reading. **


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